To record the data in the IRESite database we use a MySQL relational database as the storage engine. The data are stored within the SQL tables which consist of rows and columns. The rows are numbered consecutively by the MySQL driver. Thus, the numbers/identifiers shown below are the internal SQL row numbers as well.

When referring to an individual IRESite record or to a group of records you have the choice of several identifiers which are either unique for a single record or group together multiple records (being similar in some respect). You can handcraft URL link which will point t a single record (EMCV virus record with IRESite Id=140) or even to a group of records containing same IRES sequence (EMCV IRES based records with IRESite IRES Seq Id=1271) or even to a group of records having similar IRES name albeit different sequence (all EMCV IRES based records) and finally, you can point at once to (all records with experimentally determined secondary structure).

The IRESite Id is a number unique for any studied RNA transcript (of a cellular gene, viral genomic +RNA, viral subgenomic mRNA or even a plasmid transcript) sequence produced in a specific organism or in an in vitro system. Using this identifier you can get a list of experiments which tested translatability of the particular transcript in a certain organism or translation system (e.g. in rabbit reticulocyte lysate) or the access the summary record based on the naturally occuring viral/cellular transcript bearing this IRES. The number corresponds to a row number within the table named nucleic_acids and this is the id number you see most often (when browsing our database or vieving a single record).

The IRESite IRES Id is a unique number for any IRES region. Usually, when citing records in our database you should use "IRESite IRES Id" to refer to an individual IRES entry. Only in special cases you might want to refer to a certain group of records which share some attribute. Such attributes are the "primary sequence" or the "secondary structure" of either the underlying nucleic sequence/structure or just its part, i.e. IRES sequence/structure. Thus, the IRESite IRES Exp Id number corresponds to the row number within the table named iress.

The IRESite IRES Seq Id is a unique number for sequence of a certain IRES element located within any mRNA/+RNA molecule. When searching the IRESite using this identificator as the key you will receive all records which share this sequence denoted as the IRES segment. In other words, for all these records exactly this sequence was defined using IRES start and IRES stop co-ordinates. Beware, by a simple lookup of this "IRESite IRES Seq Id" number you will not find records which contain this IRES just as a substring! Instead, what you get is a list of records in which case exactly this sequence substring was labeled as IRES. The number corresponds to the row number within the table named sequences.

The IRESite IRES Struct Id is a unique number for a group of records containing exactly the same secondary structure within the IRES region. As already mentioned the region itself is defined by IRES start and IRES stop co-ordinates The number corresponds to the row number within the table named structures.

The IRESite Seq Id is a unique number for any unique sequence of a nucleic acid. Simply, all records referring to the same IRESite Seq Id have exactly the same end-to-end sequence. The difference of this identificator from IRESite IRES Seq Id is that this attribute describes the whole underlying nucleic acid (mRNA/+RNA) molecule whereas the IRESite IRES Seq Id identificator (see above) describes the sequence of the IRES element. All these sequence_id numbers (IRESite Seq Id, IRESite IRES Seq Id) correspond to a row id number within the table named sequences.

The IRESite 2DExp Id is a unique number for an experiment describing a secondary structure of a certain region of underlying nucleic acid sequence. The secondary structure is known to be affected by many parameters. The IRESite records only the most important ones: ion concentrations, pH, the temperature, names of the enzymes used to probe the secondary structure. The number corresponds to the row number within the table named ss_experiments.

The IRESite 2DExp Struct Id is a unique number for any distinct secondary structure. The secondary structure is typically a relatively short region of the underlying nucleic acid sequence and in principle does not have to overlap with the IRES element (although the purpose of this database is to collect the IRES structures and therefore it mostly will overlap with the IRES containing region quite well). The number corresponds to the row number within the table named structures. Similarly, IRESite 2DExp Seq Id is unique for the primary sequence of the region mapped for presence of secondary structures.

Last change to the database: 2015-04-16 16:45:23 GMT+1